Methanosarcina baikalica sp. nov., a new methanogenic archaea isolated from surface bottom sediments of Lake Baikal

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Abstract

A new methane-forming archaeon strain Z-7115T was isolated from the bottom sediments of the freshwater Lake Baikal (Eastern Siberia, Russia). Morphologically, the strain is represented by non-motile coccoid cells 0.5–3 µm in size, collected in packets of 2–4 and their small aggregates. The strain uses methanol, mono-, di-, trimethylamine and acetate as energy substrates for methanogenesis. The cells grow at a temperature of 15–35°C (optimum 25°C), pH 6.3–7.5 (optimum pH 7.3) and are tolerant to NaCl concentrations < 0.1 M. The G + C content of genomic DNA is 40.76 mol. %. According to the 16S rRNA gene analysis, the new isolate belongs to the genus Methanosarcina, having a similarity level of 98.51% with the closest species of this genus M. siciliae T4/MT . The average nucleotide similarity (ANI) between the genomes of strains Z-7115T and M. siciliae T4/MT was 83.8%. The virtual assessment of the hybridization of the genomes of these two strains was 23.3%. Based on the data of phylogenetic analysis and morpho-physiological properties, it is proposed to classify the isolated strain Z-7115T (=JCM 39438, =VKM B-3565) as a new species Methanosarcina baikalica sp. nov.

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About the authors

T. N. Zhilina

Research Center of Biotechnology of the Russian Academy of Sciences

Author for correspondence.
Email: Zhilinat@mail.ru

Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

A. Yu. Merkel

Research Center of Biotechnology of the Russian Academy of Sciences

Email: Zhilinat@mail.ru

Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

T. V. Kolganova

Research Center of Biotechnology of the Russian Academy of Sciences

Email: lichoradkin43@gmail.com

Skryabin Institute of Bioengineering

Russian Federation, Moscow, 119071

V. E. Trubitsyn

Pushchino Research Center for Biological Research of the Russian Academy of Sciences

Email: lichoradkin43@gmail.com
Russian Federation, Pushchino, 142290

V. A. Shcherbakova

Pushchino Research Center for Biological Research of the Russian Academy of Sciences

Email: lichoradkin43@gmail.com
Russian Federation, Pushchino, 142290

N. E. Suzina

Pushchino Research Center for Biological Research of the Russian Academy of Sciences

Email: lichoradkin43@gmail.com
Russian Federation, Pushchino, 142290

N. V. Pimenov

Research Center of Biotechnology of the Russian Academy of Sciences

Email: Zhilinat@mail.ru

Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

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2. Fig. 1. Comparison of methanogenesis (blue columns) and acetogenesis (yellow columns) processes on different methanogenesis substrates in Lake Baikal samples above gas hydrates (GR-1, GR-2) and oil show zones (BC-6, GG-6).

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3. Fig. 2. Morphology of cells of strain Z-7115T: a ‒ light microscope, phase contrast, scale mark ‒ 5 μm; b ‒ electron microscope, scale mark ‒ 1 μm.

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4. Fig. 3. Phylogenetic tree based on 16S rRNA gene sequences (a) and 53 conserved single-copy marker genes (b) (Chaumeil et al., 2022). The tree was reconstructed by the maximum-likelihood method using IQ-TREE 2.2.0.3 software (Minh et al., 2020). Bootstrap values ​​are shown at the nodes above. Scale bar is 0.1 substitutions per nucleotide position.

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5. Fig. 4. Ordered heat map constructed from the distribution matrix of ANI coefficients between genomes of the genus Methanosarcina.

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